data_VKH
# 
_chem_comp.id                                    VKH 
_chem_comp.name                                  "(1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C7 H16 N O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2021-05-25 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        178.206 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VKH 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7OP6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
VKH N1  N1  N 1 1 N N N N N N -19.284 59.521 50.068 -2.090 1.092  -1.238 N1  VKH 1  
VKH C2  C1  C 0 1 N N R N N N -19.860 57.550 48.180 1.584  0.653  -0.397 C2  VKH 2  
VKH C4  C2  C 0 1 N N R N N N -19.194 59.741 47.094 0.405  -1.529 -0.098 C4  VKH 3  
VKH C5  C3  C 0 1 N N R N N N -18.042 59.749 48.080 -0.944 -0.817 -0.219 C5  VKH 4  
VKH C6  C4  C 0 1 N N N N N N -17.914 61.215 48.469 -1.413 -0.374 1.169  C6  VKH 5  
VKH O2  O1  O 0 1 N N N N N N -20.870 58.395 48.793 2.545  1.547  0.168  O2  VKH 6  
VKH C7  C5  C 0 1 N N S N N N -18.221 58.799 49.294 -0.795 0.408  -1.122 C7  VKH 7  
VKH O6  O2  O 0 1 N N N N N N -19.161 61.944 48.357 -2.747 0.128  1.083  O6  VKH 8  
VKH O4  O3  O 0 1 N N N N N N -18.862 60.321 45.818 0.842  -1.943 -1.394 O4  VKH 9  
VKH C3  C6  C 0 1 N N R N N N -19.653 58.335 46.874 1.434  -0.573 0.506  C3  VKH 10 
VKH O3  O4  O 0 1 N N N N N N -20.884 58.609 46.219 0.997  -0.159 1.802  O3  VKH 11 
VKH C1  C7  C 0 1 N N N N N N -18.583 57.292 49.046 0.235  1.365  -0.517 C1  VKH 12 
VKH H1  H1  H 0 1 N N N N N N -19.502 59.006 50.897 -2.335 1.500  -0.348 H1  VKH 13 
VKH H4  H4  H 0 1 N N N N N N -20.303 56.575 47.930 1.918  0.338  -1.385 H4  VKH 14 
VKH H5  H5  H 0 1 N N N N N N -20.025 60.308 47.539 0.299  -2.403 0.545  H5  VKH 15 
VKH H6  H6  H 0 1 N N N N N N -17.127 59.451 47.548 -1.678 -1.499 -0.650 H6  VKH 16 
VKH H7  H7  H 0 1 N N N N N N -17.568 61.272 49.512 -1.388 -1.225 1.849  H7  VKH 17 
VKH H8  H8  H 0 1 N N N N N N -17.171 61.688 47.810 -0.753 0.409  1.542  H8  VKH 18 
VKH H9  H9  H 0 1 N N N N N N -21.115 58.035 49.637 3.426  1.161  0.274  H9  VKH 19 
VKH H10 H10 H 0 1 N N N N N N -17.290 58.824 49.879 -0.461 0.093  -2.111 H10 VKH 20 
VKH H11 H11 H 0 1 N N N N N N -19.023 62.849 48.611 -3.110 0.428  1.928  H11 VKH 21 
VKH H12 H12 H 0 1 N N N N N N -18.568 61.216 45.943 1.693  -2.403 -1.394 H12 VKH 22 
VKH H13 H13 H 0 1 N N N N N N -18.953 57.797 46.218 2.395  -1.080 0.592  H13 VKH 23 
VKH H14 H14 H 0 1 N N N N N N -21.317 57.792 46.003 1.602  0.450  2.246  H14 VKH 24 
VKH H15 H15 H 0 1 N N N N N N -18.807 56.753 49.978 -0.099 1.681  0.471  H15 VKH 25 
VKH H2  H2  H 0 1 N N N N N N -18.954 60.431 50.318 -2.025 1.819  -1.935 H2  VKH 26 
VKH H16 H16 H 0 1 N N N N N N -17.799 56.755 48.492 0.341  2.239  -1.161 H16 VKH 27 
VKH H3  H3  H 0 1 N N N N N N -20.106 59.608 49.504 -2.798 0.427  -1.510 H3  VKH 28 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
VKH O4 C4  SING N N 1  
VKH O3 C3  SING N N 2  
VKH C3 C4  SING N N 3  
VKH C3 C2  SING N N 4  
VKH C4 C5  SING N N 5  
VKH C5 C6  SING N N 6  
VKH C5 C7  SING N N 7  
VKH C2 O2  SING N N 8  
VKH C2 C1  SING N N 9  
VKH O6 C6  SING N N 10 
VKH C1 C7  SING N N 11 
VKH C7 N1  SING N N 12 
VKH N1 H1  SING N N 13 
VKH C2 H4  SING N N 14 
VKH C4 H5  SING N N 15 
VKH C5 H6  SING N N 16 
VKH C6 H7  SING N N 17 
VKH C6 H8  SING N N 18 
VKH O2 H9  SING N N 19 
VKH C7 H10 SING N N 20 
VKH O6 H11 SING N N 21 
VKH O4 H12 SING N N 22 
VKH C3 H13 SING N N 23 
VKH O3 H14 SING N N 24 
VKH C1 H15 SING N N 25 
VKH H2 N1  SING N N 26 
VKH C1 H16 SING N N 27 
VKH H3 N1  SING N N 28 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
VKH InChI            InChI                1.03  "InChI=1S/C7H15NO4/c8-4-1-5(10)7(12)6(11)3(4)2-9/h3-7,9-12H,1-2,8H2/p+1/t3-,4-,5+,6+,7+/m0/s1" 
VKH InChIKey         InChI                1.03  FGLYJEXIORSHSO-PAMBMQIZSA-O                                                                    
VKH SMILES_CANONICAL CACTVS               3.385 "[NH3+][C@H]1C[C@@H](O)[C@@H](O)[C@H](O)[C@H]1CO"                                              
VKH SMILES           CACTVS               3.385 "[NH3+][CH]1C[CH](O)[CH](O)[CH](O)[CH]1CO"                                                     
VKH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@@H]([C@H]([C@@H]([C@@H]1O)O)O)CO)[NH3+]"                                          
VKH SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(C1O)O)O)CO)[NH3+]"                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           VKH 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[(1~{S},2~{R},3~{R},4~{R},5~{R})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]azanium" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VKH "Create component"   2021-05-25 PDBE 
VKH "Other modification" 2021-07-19 EBI  
VKH "Other modification" 2021-07-20 PDBE 
VKH "Other modification" 2021-07-21 PDBE 
VKH "Initial release"    2022-02-02 RCSB 
VKH "Modify PCM"         2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 VKH GLU None "Covalent chemical modification" "Amino-acid side chain" "Any position" C1 OE1 ? ? 
2 VKH GLU None "Covalent chemical modification" "Amino-acid side chain" "Any position" C1 OE2 ? ? 
# 
